Package: CancerMutationAnalysis

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerMutationAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerMutationAnalysis_1.29.0.tar.gz

StartedAt: 2020-01-16 02:28:51 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:33:51 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 300.1 seconds

RetCode: 0

Status:  OK

CheckDir: CancerMutationAnalysis.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CancerMutationAnalysis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CancerMutationAnalysis_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CancerMutationAnalysis.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CancerMutationAnalysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CancerMutationAnalysis’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CancerMutationAnalysis’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘qvalue’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ebfdr: no visible global function definition for ‘density’
ebfdr: no visible global function definition for ‘plot’
ebfdr: no visible global function definition for ‘text’
ebfdr: no visible global function definition for ‘abline’
ebfdr: no visible global function definition for ‘rug’
ebfdr: no visible global function definition for ‘hist’
p2q: no visible global function definition for ‘qvalue’
perm.null.het.p.values: no visible global function definition for
  ‘dhyper’
perm.null.p.values: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  abline density dhyper hist plot qvalue rug text
Consider adding
  importFrom("graphics", "abline", "hist", "plot", "rug", "text")
  importFrom("stats", "density", "dhyper")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
cma.set.sim 53.291 15.671  69.033
cma.fdr     36.599 19.958  61.456
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CancerMutationAnalysis.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CancerMutationAnalysis
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CancerMutationAnalysis’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c get.cdf.het.berns.c -o get.cdf.het.berns.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CancerMutationAnalysis.so get.cdf.het.berns.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CancerMutationAnalysis/00new/CancerMutationAnalysis/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CancerMutationAnalysis)

name	user	system	elapsed
cma.fdr	36.599	19.958	61.456
cma.scores	0.716	0.088	0.804
cma.set.sim	53.291	15.671	69.033
cma.set.stat	3.144	0.440	3.586
combine.sims	0.000	0.001	0.000
extract.sims.method	0.001	0.000	0.001